Journal of Magnetic Resonance Open最新文献

Protein dynamics due to flexible linkers connecting otherwise rigid domains may be critical for the functioning of a variety of biological systems, ranging from membrane transporters to calcium-signaling and the formation of intercellular junctions. Considering that NMR spectroscopy is extremely powerful to characterize dynamics at various time scales, this manuscript brings an overview of the main strategies that have been employed to characterize inter-domain dynamics in relevant biological systems. Emphasis was given to the calcium binding proteins: calmodulin, cadherin, and the Na⁺/Ca²⁺ exchanger calcium-sensor domain. The introduction of paramagnetic centers in diamagnetic proteins is seen as key to obtaining unambiguous information about inter-domain dynamics. This is because the self-alignment of one of the domains in multi-domain proteins avoids the problem of dealing with alignment tensor fluctuations in dynamic systems. The combination of residual dipolar couplings (RDCs) and pseudocontact shifts (PCSs) with computational strategies aiming to provide an ensemble description of protein dynamics is seen as the most powerful strategy to gain detailed atomistic information on inter-domain motions. It is noteworthy that the cadherin ectodomains and the Na⁺/Ca²⁺ exchanger calcium sensor respond in the same way upon calcium-binding: in the absence of calcium the two domains are flexibly linked to one another and may preferentially sample kinked inter-domain arrangements, while calcium binding stabilizes a rigid and extended inter-domain arrangement. It is thus remarkable that nature chose the same molecular mechanism to promote two very different biological functions that are triggered by calcium signaling: intercellular adhesion by the formation of cadherin dimers and the allosteric regulation of a membrane transporter in the case of the Na⁺/Ca²⁺ exchanger.

The data obtained from a scanner for Magnetic Resonance Spectroscopy (MRS) is three-dimensional (3D) since the FID data from the scanner has spectrum values which are 2D complex numbers and 1D time values. This paper describes an MRS frequency-based post-processing method that has the advantage that it quickly determines the values needed for metabolite intensities and concentrations, even for most overlapping spectral terms.

The method of this paper does not depend on area under a curve or a user-chosen basis set. As few as three valid points corresponding to a peak on the spectral curve are all that is needed, other than similar information on a reference metabolite, for concentration determination of the associated metabolite. All four of the key values of peak location, amplitude, phase angle, and damping constant are determined simultaneously with high accuracy, dependent upon noise, and with computational simplicity from only three complex-valued constants. The theory behind mdMRS uses the knowledge that the projection of the 3D spectrum to the complex plane is a simple circle. Several concepts from complex variables theory are important, such as the Linear Fractional Transformation (LFT) that maps the frequency axis to that circle. The duality linking an LFT with a 2 $\times$ 2 Moebius matrix enables a fast iteration process that sharpens the four key value estimates on each iteration. The iteration removes all other terms when considering one of them. Applied to initial estimates, this leads to increasingly accurate output.

To be useful to clinicians and to researchers developing treatments based on metabolite concentrations, the goal for post-processing of the data include both fast and accurate computations, with speed sufficient to provide results “on console” and output provided as concentrations. Besides the number of protons associated with a metabolite, concentrations are determined using both amplitude and damping constant values. Since the methods of mdMRS provide both of those characteristics simultaneously, the time from data collection to metabolite concentration output is minimized. The name of this new post-processing method was chosen since the attributes of the method help bring that goal closer to reality for Medical Doctors.

In light of the growing interest in-vivo deuterium metabolic imaging, hyperpolarized ¹³C, ¹⁵N, ³He, and ¹²⁹Xe imaging, as well as ³¹P spectroscopy and imaging in large animals on clinical MR scanners, we demonstrate the use of a (radio)frequency converter system to allow X-nuclear MR spectroscopy (MRS) and MR imaging (MRI) on standard clinical MRI scanners without multinuclear capability. This is not only an economical alternative to the multinuclear system (MNS) provided by the scanner vendors, but also overcomes the frequency bandwidth problem of some vendor-provided MNSs that prohibit users from applications with X-nuclei of low magnetogyric ratio, such as deuterium (6.536 MHz/Tesla) and ¹⁵N (-4.316 MHz/Tesla). Here we illustrate the design of the frequency converter system and demonstrate its feasibility for ³¹P (17.235 MHz/Tesla), ¹³C (10.708 MHz/Tesla), and ¹⁵N MRS and MRI on a clinical MRI scanner without vendor-provided multinuclear hardware.

Transition metal ion-containing oxidoreductases, which carry out long-distance electron transfer reactions, are a large family of metalloproteins that are widely distributed in nature. The metal ions are either present as mononuclear centers or are organized in clusters. One of the metal cofactors is the active site of the enzyme where the substrate is converted to a product, while the others serve as electron transfer centers. Metal cofactors are paramagnetic in certain protein redox states and may additionally exhibit different relaxation rates and weak superexchange interactions transferred via intraprotein electron transfer pathways. Cu-containing nitrite reductase and Mo-containing aldehyde oxidoreductase are two representative examples of oxidoreductases in which these phenomena occur, making them interesting systems to study using electron magnetic resonance techniques. We summarize here several X-band Continuous-Wave Electron Paramagnetic Resonance (CW-EPR) studies that have allowed insights into structural and functional aspects of these two proteins and may help characterize closely related systems.

Staphylococcus aureus CzrA is a paradigmatic member of the ArsR family of transcriptional metalloregulators, which are critical for the bacterial response to stress. Zinc binding to CzrA, which induces DNA derepression, is entropically driven, as shown by calorimetry. A detailed equilibrium dynamics study of different allosteric states of CzrA revealed that zinc induces an entropy redistribution that controls for DNA binding regulation; however, this change in conformational entropy only accounts for a small net contribution to the total entropy. This difference between the change in conformational entropy vs. total entropy of zinc binding implies a significant contribution of solvent molecule rearrangements to this equilibrium. However, the absence of major structural changes suggests that solvent rearrangements occur mainly on the protein surface and/or from zinc desolvation, concomitant with a dynamical redistribution of conformational entropy. Previous results also suggest that zinc binding not only leads to a redistribution of protein internal dynamics, but also release of water molecules from the protein surface. In turn, these water molecules may make a significant contribution to the allosteric response that results in dissociation from the DNA.

Quantifying the differential hydration of two conformational states that share very similar crystal structures and then correlating this with the protein's solvent entropy change constitutes an unresolved problem, even when thermodynamics suggest a significant contribution of solvent entropy. Here, we present different avenues to dissect hydration dynamics in a metal-binding transcriptional regulator that provide different insights into this complex problem. We explore primary solution NMR tools for probing protein–water interactions: the laboratory frame nuclear Overhauser effect (NOE) and its rotating frame counterpart (ROE) between long-lived water molecules and the protein residues. The wNOE/wROE ratio is a promising tool for the detection of hydration dynamics near the surface of a protein in a site-specific manner, minimizing contamination from bulk solvent. Molecular dynamics simulations and computational methods designed to provide a spatially resolved picture of solvent thermodynamics were also employed to provide a more complete panorama of solvent redistribution.

This Primer critically reviews the possibilities and limitations of probing the short-range structure of an oxide-based glass by routine magic-angle spinning (MAS) or triple-quantum MAS (3QMAS) nuclear magnetic resonance (NMR) experiments. We briefly outline the structural features of oxide-based glasses and the basics of solid-state NMR. Besides suggesting guidelines for selecting favorable experimental conditions and important considerations for recording high-quality MAS NMR spectra amenable for subsequent analysis, we review options for extracting NMR observables and their distributions from spins-1/2 as well as half-integer spin quadrupolar nuclei. Considering that the isotropic chemical shift remains the primary probe of local structure by MAS NMR, we thoroughly review its dependence on the short-range oxide-based glass parameters from the viewpoint of a very simple and intuitive but qualitative model. The utility of deconvolutions of notably ²⁹Si and ³¹P MAS NMR spectra are discussed critically. We also suggest alternative yet qualitative analysis options that are available whenever MAS NMR spectral deconvolutions are not warranted without additional information, which incidentally applies to a majority of modern multicomponent glasses.

Nuclear Magnetic Resonance (NMR) plays a central role in developing quantum information sciences and technologies. Key features such as its non-invasive nature and the ability to process information on nuclear spins by versatile quantum control designs with electromagnetic fields, have made NMR to become a powerful technique for sensing systems from atomic and molecular scales with spectroscopy to millimeters in imaging. This brief overview provides quantum sensing tools with which we are contributing from Latin America, by combining quantum dynamical control and estimation strategies with NMR methods to probe physical, chemical, and biological processes. It introduces the basic and key concepts on how controlled spin-sensors can monitor the correlation dynamics of their environment, and selectively and optimally infer its relevant parameters. Then these concepts are illustrated with state-of-the-art implementations for characterizing (i) biological tissue microstructure with diffusion weighting imaging, (ii) quantum information dynamics and scrambling in out-of-equilibrium systems with solid-state NMR quantum simulations, and (iii) molecular structures by selective estimation of spin–spin couplings and online learning control designs with experimental proposals. We expect these concepts will motivate the development of quantum dynamical control of spin sensors to monitor systems in a variety of fields, and in particular to exploit the non-invasive strength of NMR, e.g. in biomedical diagnosis.

At low magnetic fields (<1 T), the low loss of radio frequency (RF) coils can cause RF pulses, in magnetic resonance (MR) experiments, to suffer from long rise and fall times. When severe, long rise and fall times can result in RF pulses with undesirable and/or unexpected shapes, lengths, and amplitudes leading to inadequate spin control during an MR experiment. Experimentally, the lack of spin control becomes evident in the shape of the nutation curve and the inversion efficiency, the degree to which full inversion is accomplished following a 180° pulse. Lowering the quality factor (Q) of tuned coil is shown to reduce the duration of the rise and fall times. The effects of long rise and fall times on the spin behavior during an MR experiment is explored. It is shown that the inversion efficiency can be used to provide a threshold that ensures high fidelity pulses with adequate spin control.

In-cell NMR spectroscopy has emerged as a powerful tool to evaluate protein conformations and dynamics in the native environment of live cells. Here we extend these studies to a multicellular developing vertebrate. Zebrafish (Danio rerio) embryos are complex organisms with dynamic tissue organization and may be well suited for the high resolution NMR analysis of microinjected, isotopically enriched proteins. We used the intrinsically disordered protein Alpha-synuclein (aSyn) as a test model. aSyn has been thoroughly evaluated inside bacterial and mammalian cells, providing good reference points for NMR comparisons and the critical analysis of the advantages and disadvantages of the zebrafish system. High resolution 2D ¹H-¹⁵N NMR showed that aSyn in zebrafish embryos had the same conformational and biological features previously observed in mammalian cells, including conserved interactions with cellular biomolecules and the establishment of physiological protein post-translational modifications. A direct comparative analysis of gamma-synuclein (gSyn), a naturally occurring homolog of aSyn, in bacteria, mammalian cells and zebrafish embryos confirmed these observations. Our results showed that high resolution in-cell NMR is attainable in embryonic cells within the native environment of a live animal. This system provides more physiological cellular environments for high resolution, in situ protein biophysical studies.

Double stranded RNA binding domains (dsRBDs) are ubiquitous in all kingdoms of life. They can participate both in RNA and protein recognition and are usually present in multiple copies in multidomain proteins. We analyzed the linkers between dsRBDs in different proteins and found that sequences corresponding to plant proteins have a highly conserved linker length. In order to assess the importance of linker length in the conformational freedom of double dsRBD plant proteins, we introduced lanthanide binding tags (LBTs) in different positions of the dsRBD containing protein HYL1 from Arabidopsis thaliana. These constructs were used to obtain conformational restraints from Double electron–electron resonance (DEER) measurements on doubly labeled proteins and from paramagnetic relaxation enhancement (PRE) in single labeled samples. Fitting the experimental datasets to a computational model of the ensemble created by allowing freedom to the linker region we found that the domains tend to explore a particular region of the allowed conformational space. The high conservation in linker length suggests that this restricted conformational sampling is functional, possibly hindering HYL1-dsRBD2 from contacting the substrate dsRNA and allowing it to participate in protein-protein interactions.